title: Probe signal correction for differential methylation hybridization experiments.
abstract: BACKGROUND
  Non-biological signal (or noise) has been the bane of microarray analysis. Hybridization effects related to probe-sequence composition and DNA dye-probe interactions have been observed in differential methylation hybridization (DMH) microarray experiments as well as other effects inherent to the DMH protocol.
  
  
  RESULTS
  We suggest two models to correct for non-biologically relevant probe signal with an overarching focus on probe-sequence composition. The estimated effects are evaluated and the strengths of the models are considered in the context of DMH analyses.
  
  
  CONCLUSIONS
  The majority of estimated parameters were statistically significant in all considered models. Model selection for signal correction is based on interpretation of the estimated values and their biological significance.
authors.affiliation: Human Cancer Genetics Program, OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA. potterdp@gmail.com
authors.forename: Dustin P
authors.initials: DP
authors.lastname: Potter
authors.forename: Pearlly
authors.initials: P
authors.lastname: Yan
authors.forename: Tim H M
authors.initials: TH
authors.lastname: Huang
authors.forename: Shili
authors.initials: S
authors.lastname: Lin
mesh_terms: D001483:Base Sequence; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D002232:Carbocyanines / Q000378:metabolism; D045744:Cell Line, Tumor; D019175:DNA Methylation; D015342:DNA Probes; D005260:Female; D005456:Fluorescent Dyes / Q000378:metabolism; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D008745:Methylation; D008957:Models, Genetic; D015233:Models, Statistical; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D017422:Sequence Analysis, DNA; D015398:Signal Transduction
chemical_list: D002232:Carbocyanines; D015342:DNA Probes; D005456:Fluorescent Dyes; C089187:cyanine dye 3